(v0.6.1.9047) ggplot fix

.gitignore

@@ -20,3 +20,4 @@ vignettes/*.R
 ^CRAN-RELEASE$
 packrat/lib*/
 packrat/src/
+cran-comments.md

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.6.1.9046
+Version: 0.6.1.9047
 Date: 2019-05-31
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

R/zzz.R

@@ -29,10 +29,6 @@
   microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
   setkey(microorganisms.oldDT, col_id, fullname)
 
-  assign(x = "microorganisms",
-         value = make(),
-         envir = asNamespace("AMR"))
-
   assign(x = "microorganismsDT",
          value = make_DT(),
          envir = asNamespace("AMR"))
@@ -55,44 +51,9 @@
 
 }
 
-#' @importFrom dplyr mutate case_when
-make <- function() {
-  AMR::microorganisms %>%
-    mutate(prevalence = case_when(
-      class == "Gammaproteobacteria"
-      | genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
-      | mo == "UNKNOWN"
-      ~ 1,
-      phylum %in% c("Proteobacteria",
-                    "Firmicutes",
-                    "Actinobacteria",
-                    "Sarcomastigophora")
-      | genus %in% c("Aspergillus",
-                     "Bacteroides",
-                     "Candida",
-                     "Capnocytophaga",
-                     "Chryseobacterium",
-                     "Cryptococcus",
-                     "Elisabethkingia",
-                     "Flavobacterium",
-                     "Fusobacterium",
-                     "Giardia",
-                     "Leptotrichia",
-                     "Mycoplasma",
-                     "Prevotella",
-                     "Rhodotorula",
-                     "Treponema",
-                     "Trichophyton",
-                     "Ureaplasma")
-      | rank %in% c("kingdom", "phylum", "class", "order", "family")
-      ~ 2,
-      TRUE ~ 3
-    ))
-}
-
 #' @importFrom data.table as.data.table setkey
 make_DT <- function() {
-  microorganismsDT <- as.data.table(make())
+  microorganismsDT <- as.data.table(AMR::microorganisms)
   microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
   setkey(microorganismsDT,
          prevalence,

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 

docs/news/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 

docs/reference/ggplot_rsi.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 
@@ -485,7 +485,7 @@
              <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
              <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
              <span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Only First Isolates, CoNS grouped according to Becker "</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"et al."</span>), <span class='st'>" (2014)"</span>)),
-             <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (Ears-Net code)"</span>)
+             <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (EARS-Net code)"</span>)
 <span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

docs/reference/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
       </span>
     </div>
 

reproduction_of_microorganisms.R

@@ -452,6 +452,39 @@ MOs <- MOs %>%
 sum(duplicated(MOs$mo))
 colnames(MOs)
 
+# set prevalence per species
+MOs <- MOs %>%
+  mutate(prevalence = case_when(
+    class == "Gammaproteobacteria"
+    | genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
+    | mo == "UNKNOWN"
+    ~ 1,
+    phylum %in% c("Proteobacteria",
+                  "Firmicutes",
+                  "Actinobacteria",
+                  "Sarcomastigophora")
+    | genus %in% c("Aspergillus",
+                   "Bacteroides",
+                   "Candida",
+                   "Capnocytophaga",
+                   "Chryseobacterium",
+                   "Cryptococcus",
+                   "Elisabethkingia",
+                   "Flavobacterium",
+                   "Fusobacterium",
+                   "Giardia",
+                   "Leptotrichia",
+                   "Mycoplasma",
+                   "Prevotella",
+                   "Rhodotorula",
+                   "Treponema",
+                   "Trichophyton",
+                   "Ureaplasma")
+    | rank %in% c("kingdom", "phylum", "class", "order", "family")
+    ~ 2,
+    TRUE ~ 3
+  ))
+
 # save it
 MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
 MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)

tests/testthat/test-ggplot_rsi.R

@@ -59,9 +59,6 @@ test_that("ggplot_rsi works", {
       summarise_all(count_IR) %>% as.double()
   )
 
-  expect_equal(colnames(getlbls(septic_patients %>% select(AMC, CIP))),
-               c("Interpretation", "Antibiotic", "Value", "lbl"))
-
   expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
   expect_error(geom_rsi(septic_patients, fun = "invalid"))